Lesion bypass by S. cerevisiae Pol ζ alone

DNA polymerase zeta (Pol ζ) participates in translesion synthesis (TLS) of DNA adducts that stall replication fork progression. Previous studies have led to the suggestion that the primary role of Pol ζ in TLS is to extend primers created when another DNA polymerase inserts nucleotides opposite lesions. Here we test the non-exclusive possibility that Pol ζ can sometimes perform TLS in the absence of any other polymerase. To do so, we quantified the efficiency with which S. cerevisiae Pol ζ bypasses abasic sites, cis-syn cyclobutane pyrimidine dimers and (6-4) photoproducts. In reactions containing dNTP concentrations that mimic those induced by DNA damage, a Pol ζ derivative with phenylalanine substituted for leucine 979 at the polymerase active site bypasses all three lesions at efficiencies between 27 and 73%. Wild-type Pol ζ also bypasses these lesions, with efficiencies that are lower and depend on the sequence context in which the lesion resides. The results are consistent with the hypothesis that, in addition to extending aberrant termini created by other DNA polymerases, Pol ζ has the potential to be the sole DNA polymerase involved in TLS.     

酿酒酵母S.cerevisiae高密度培养条件优化研究

考察了培养基组成和培养条件对酿酒酵母Saccharomyces cerevisiae发酵的影响。以TB培养基为初始培养基,通过正交实验设计优化培养基组成,确定了影响酵母细胞产量最主要的因素是葡萄糖,最适培养基组成为:酪蛋白胨15 g/L,酵母粉25 g/L,葡萄糖30 g/L,KH2PO42.4g/L,K2HPO4.3H2O 16.34 g/L。并确定了最佳培养条件:温度30℃,转速150 r/min。采用优化培养基及培养条件下进行发酵,菌液最高OD600值和细胞密度分别达15.82和2.03×108/mL,比优化前分别提高24.2%和22.0%。     

Autophagy across the eukaryotes: Is S. cerevisiae the odd one out?

Autophagy is conserved throughout the eukaryotes and for many years, work in Saccharomyces cerevisiae has been at the forefront of autophagy research. However as our knowledge of the autophagic machinery has increased, differences between S. cerevisiae and mammalian cells have become apparent. Recent work in other organisms, such as the amoeba Dictyostelium discoideum, indicate an autophagic pathway much more similar to mammalian cells than S. cerevisiae, despite its earlier evolutionary divergence. S. cerevisiae therefore appear to have significantly specialized, and the autophagic pathway in mammals is much more ancient than previously appreciated, which has implications for how we interpret data from organisms throughout the eukaryotic tree.     

What Can Causal Networks Tell Us about Metabolic Pathways?

Graphical models describe the linear correlation structure of data and have been used to establish causal relationships among phenotypes in genetic mapping populations. Data are typically collected at a single point in time. Biological processes on the other hand are often non-linear and display time varying dynamics. The extent to which graphical models can recapitulate the architecture of an underlying biological processes is not well understood. We consider metabolic networks with known stoichiometry to address the fundamental question: “What can causal networks tell us about metabolic pathways?”. Using data from an Arabidopsis BaySha population and simulated data from dynamic models of pathway motifs, we assess our ability to reconstruct metabolic pathways using graphical models. Our results highlight the necessity of non-genetic residual biological variation for reliable inference. Recovery of the ordering within a pathway is possible, but should not be expected. Causal inference is sensitive to subtle patterns in the correlation structure that may be driven by a variety of factors, which may not emphasize the substrate-product relationship. We illustrate the effects of metabolic pathway architecture, epistasis and stochastic variation on correlation structure and graphical model-derived networks. We conclude that graphical models should be interpreted cautiously, especially if the implied causal relationships are to be used in the design of intervention strategies.     

Can Continuous Glucose Monitoring Provide Objective Documentation of Hypoglycemia Unawareness?

ObjectiveTo establish criteria defining hypoglycemia as detected by the continuous glucose monitoring system (CGMS) in patients with type 1 diabetes that best predict hypoglycemia unawareness (HUN), established by a validated questionnaire.MethodsAdult patients were selected for inclusion in this study if they had long-standing type 1 diabetes, a fasting level of C peptide of ≤ 0.6 ng/mL, commitment to achieving glycemic control, and a hemoglobin A1c value no higher than 9%. After clinical data and self-monitoring of plasma glucose data were collected, patients underwent a 72-hour glucose monitoring session with use of a Medtronic-MiniMed CGMS. The presence of HUN was determined by a questionnaire. Factors independently associated with HUN were estimated by multivariate independent analysis.ResultsOur study group consisted of 60 patients (33 women and 27 men) who ranged in age from 18 to 84 years (mean, 50.4) and had had diabetes for 5 to 56 years (mean, 23.8). The best predictor of HUN was the maximal duration of hypoglycemia, as determined by the CGMS (P = 0.001). Detection of hypoglycemic episodes with a duration of more than 90 minutes identified patients who had HUN with an 88% specificity and 75% sensitivity. HUN was also significantly associated with use of angiotensin-converting enzyme inhibitors or angiotensin receptor blockers (P = 0.003) and with a longer duration of diabetes (P = 0.008).ConclusionThe CGMS can be used for objective detection of patients with HUN. (Endocr Pract. 2005; 11:83-90)     

Oosterschelde estuary (S.W. Netherlands): a self-sustaining ecosystem?

The Oosterschelde estuary has a special position among the Dutch North Sea estuaries. With relatively unpolluted water and high transparency it combines high biotic diversity and high primary and secondary production. Before 1970 a major part of the water of the rivers Rhine and Meuse flowed into the Oosterschelde. The building of a permeable storm-surge barrier (1986) decreased the exchange between Oosterschelde and North Sea. The construction of two additional dams (1987) reduced the very limited fresh water discharge on the estuary even further. The total effect of these changes was a decrease of the nutrient levels in the water column.The estuary is used intensively for culture of mussels and fishery of cockles. Both zoobenthos groups use together up to 60% (in the western part) of the organic food available in the Oosterschelde estuary. The storm-surge barrier resulted in reduced current velocities and increased sedimentation, accompanied by higher transparency, hence accelerating primary production. This phenomenon is counteracted by the lowered nutrient concentrations throughout the year.In the seventies a preliminary carbon budget study indicated that a substantial import of organic carbon was required to sustain the ecosystem. Later studies did not confirm this hypothesis.In the present paper three different methods are presented to answer the question, if internal production suffices to sustain the foodweb. At first a steady state model is applied, secondly, calculations with actually measured process rates are carried out and, finally, a dynamic simulation model is used.The conclusion is drawn that, before the construction of the storm-surge barrier, primary production of organic matter by phytoplankton is much more important than import, although the latter can not be neglected as additional food source for mussels, cockles and zooplankton. The simulation model predicts that this conclusion will not have to be changed in the future. The Oosterschelde will remain largely a self-sustaining ecosystem.     

邓叔群(S.C.Teng)先生生平

1902年12月12日出生于福建省福州市。 1915年考入北京清华学堂。 1923年赴美国康奈尔大学留学取得农学士、森林学硕士学位。 1925—1928年攻读康奈尔大学植物病理学博士并被授予全美国最高科学学会 PHI-KAPPA-PHI和SIGMA-XI两枚金钥匙证章并成为其荣誉会员。 1928年回国,任岭南大学、金陵大学和中央大学一级教授。 1932—1941年历任中国科学社生物研究所、中央自然历史博物馆、中华教育文化基金董事会和中央研究院动植物研究所研究员、中央研究院林业实验研究所副所长。 1941—1946年任甘肃省水利林牧公司林业部经理。 1948年当选…     

What Insights Can Baboon Feeding Ecology Provide for Early Hominin Niche Differentiation?

Several authors have proposed that papionin baboons provide appropriate analogs for early hominin niche differentiation. Savanna-dwelling baboons and australopiths both radiated around the same time after Neogene expansion of C₄ grasslands, likely experiencing similar environmental changes and faced with solving similar ecological problems. We explore the insights baboons may provide into dietary ecology of savanna-occupying hominins. We compare dietary information from stable isotope data for feces, hair, and tooth dentine collagen of modern chacma baboons (Papio ursinus) with dietary data for Plio-Pleistocene papionins and hominins from South African savannas. Results confirm that, like the australopiths, baboons consume substantial amounts of C₄ food sources. However, the magnitude of inter- and intraindividual variation in baboon diets across different seasons and habitats is less than that from specimens of Australopithecus africanus and Paranthropus robustus analyzed to date. Hominins also consumed greater amounts of C₄ resources. Thus, though the data demonstrate that the radiation of both primate groups was closely linked with the spread of C₄ grasslands, hominins were even more extreme ecological generalists than baboons were. The absence of a fixed-diet in papionins implies that it was unlikely that the more ecologically flexible hominins evolved specializations for any one food type, an interpretation consistent with recent carbon isotope, dental microwear, and ecomorphological studies. We propose that researchers place less emphasis on resolving the foods that were most important for hominin differentiation; instead, future research should focus on questions related to ecological generalism.     

双层面调控S. cerevisiae碳流促进L-乳酸积累

摘要：【目的】调控Sacchromyces cerevisiae丙酮酸节点碳流分布促进L-乳酸积累。【方法】利用同源重组方法,将来源于Bovine的乳酸脱氢酶基因LDH整合到S. cerevisiae CEN.PK2-1C基因组中,同时敲除丙酮酸脱羧酶基因PDC1,将碳流导向L-乳酸的积累,构建了基因工程菌S. cerevisiae CEN.PK2-1C[LDH]。在此基础上,通过分析丙酮酸节点处关键酶对NADH的Km值不同,而将来源于Streptococcus pneumoniae 的NADH氧化酶(n     

Expression of Bacillus sp. β-xylosidase gene (xylB) in Saccharomyces cerevisiae

-Xylosidase gene (xylB) from Bacillus sp. was amplified and inserted between GAL10 promoter and GAL7 terminator. For the secretory production of xylB in Saccharomyces cerevisiae, in-frame fusion of the exoinulinase signal sequence (INU1s) of Kluyveromyces marxianus to the upstream of xylB was conducted. When a transformant of S. cerevisiae harboring the resulting plasmid was grown on galactose-containing medium, most of -xylosidase activity was localized in the periplasmic space of yeast and a maximum total activity reached about 2.9 unit ml^–1 at 42 h cultivation. The recombinant -xylosidase was produced as an active dimer form.     

Can Pollen Headspace Volatiles and Pollenkitt Lipids Serve as Reliable Chemical Cues for Bee Pollinators?

Chemical analysis of putative contact chemical cues for pollinators from pollen of two plant species, Ranunculus bulbosus (Ranunculaceae) and Campanula rapunculoides (Campanulaceae), showed high consistency in the qualitative and quantitative composition of pollenkitt surface lipids in all samples analyzed per species. The pollenkitt lipids of R. bulbosus included an aldehyde, fatty acid amides, saturated and unsaturated hydrocarbons, and secondary alcohols; the lipids of C. rapunculoides consisted of an aldehyde, monoketones, and β-diketones. In marked contrast, the pollen headspace volatiles showed a wide qualitative and quantitative variability among all samples per species, whereby the variability was more pronounced in R. bulbosus. Hence, the highly species-specific pollenkitt lipids may provide pollinators with more reliable information on pollen identity.     

Can Neck Circumference Predict Metabolic Syndrome? An Experience From A University Community

Objective: Neck circumference (NC) is associated with cardiovascular risk factors. The data for the measurement of the NC to predict metabolic syndrome (MetS) are limited. The objectives of this study were to determine the capability of the NC to detect MetS and to identify the optimal cutoff points of the NC among Thais.Methods: Participants who were aged ≥50 years who attended the Healthy Ageing Khon Kaen University Campus Project between March 2012 and April 2015 were recruited to this cohort study specific for atherosclerotic-related diseases. Baseline characteristics, anthropometric measures including NC, and metabolic profiles were collected. MetS was identified using the criteria of the National Cholesterol Educational Program Adult Treatment Panel III (NCEP ATP III) and International Diabetes Foundation (IDF).Results: There were 201 males and 386 females recruited for this study. The areas under the receiver operating characteristic (ROC) curves (AUCs) of NC based on the IDF criteria for females and males were 0.79 (95% confidence interval [CI] 0.75, 0.84) and 0.84 (95% CI 0.79, 0.9), respectively. For the NCEP ATP III criteria, the AUCs were 0.77 (95% CI 0.72, 0.82) in females and 0.71 (95% CI 0.64, 0.78) in males. An NC of 39 cm using IDF criteria for makes was determined as the optimal cutoff point to identify subjects with MetS. An NC of 33 cm for females was the best cutoff point for determining which subjects had MetS using both criteria.Conclusion: NC measurement and the use of established cutoff points is useful for predicting MetS in older Thai people.Abbreviations:AUC = area under the curveBMI = body mass indexCI = confidence intervalDM = diabetes mellitusHDL = high-density lipoproteinIDF = International Diabetes FoundationMetS = metabolic syndromeNC = neck circumferenceNCEP ATP III = National Cholesterol Educational Program Adult Treatment Panel IIIROC = receiver operating characteristicWC = waist circumference     

Donald S. Farner (1915–1988)

In Memoriam

Donald S. Farner (1915–1988)     

Can lacewings feed on pests in winter? (Neur.: Chrysopidae and hemerobiidae)

Some lacewings occur in winter as larvae and may be efficient predators, either under Mediterranean and mild temperate climates, or in cold greenhouses. They can be used to help controlling aphids in winter. Among chrysopids,Dichochrysa spp. overwinter as second and/or third instars; they show a low preying rate, both a moderate cold hardiness and a minimal activity threshold.Nineta pallida overwinters as first instars which have a very low activity threshold and a high cold hardiness. In hemerobiids — namely various spp. ofHemerobius, Wesmaelius, Micromus — hibernating larvae manifest prey searching and feeding activity at low temperatures. Minimal thermal thresholds may be very low in embryos and in larvae. Adults often are insensitive to photoperiod and so do not exhibit any diapause under short daylength conditions; they have a low minimal activity threshold for preying and reproducing.